You know, I have no problem with understanding thrust angle when the motor is up front. Now swap ends and make it a pusher and I get confused. Maybe looking at the motor angle from the front of the motor would make sense.

If the front of the motor is higher than the back of the motor then it has upthrust, and visa-versa. Would that be correct? Of course the effect it has on the plane is totally different. Up thrust on a tractor tries pull the nose up (climb), but up thrust on a pusher tries to pull the tail up (pitching the nose down).

It certainly makes a difference when something is at the back or the front.
You have an elevator at the back that goes up to give lift but if you have the elevator at the front, ie canard, then it goes down to give lift, however, if your motor at the back (pusher mode) is pointing down then the nose of the plane will get pushed down and if the motor is pointing up, the nose will get pushed up. If your motor is up front and is pointing down the same will occur, exept the nose will get pulled down rather than pushed.

Just got back from a wonderful morning of battling the wind. Flying into the wind at part throttle and pull up and throw full aileron and watch the Funjet spin on its tail while hovering, briefly.
Had the nearby gang at the soccer field entertained too.
Using extreme control throws to get it doing some awesome aerobatics, just too cool.
Tried all this with the Stryker and mono Twinjet and just not nearly as fun.
Don't mean to gush but it's the first flights in a couple days and it was great!

Sometime ago, Jurgen commented that the older Thunder Power PL cells I was was using and posted in a graph might not be up to the task of the Medusa 028-040-2500, so I ran it today with two different props on a new MaxAmps 3S1P 2100HV and used the digital in-flight recorder.

The graph left of the vertical gray line is an APC 6.5 x 2.9 prop and right of the line is the APC 6x4e.

The in-flight readings indicate the pack will put out 35+ amps in bursts and holds voltage at least enough to fly at half to 3/4 throttle, which is how I fly. While these packs are about 5 grams heavier than the TP's they do not heat up as much as the TP's - not an issue in the FJ that has excellent air flow, but is a real issue in some of my other planes.

At $50/pack vs. around $75+ for TP's, on a 3 for 2 cost basis, I am sold on them. YMMV.

So it looks like we still have some contention over the motor thrust angle.
I originally thought it was about whether the motor was thrusting downwards, but the first reply indicated that it was the effect on the airframe that denoted up or down thrust. Can we please get some clarity on this?

With regards to the elevon travel, I had to use the standard throws from the instructions to avoid fouling on the vertical fins with full deflection on both channels (one up and one level). My servos are easily capable of double this amount so do I just hack away at the elevons till they clear, or will this have negative consequences that I haven't thought of?

So it looks like we still have some contention over the motor thrust angle.
I originally thought it was about whether the motor was thrusting downwards, but the first reply indicated that it was the effect on the airframe that denoted up or down thrust. Can we please get some clarity on this?

With regards to the elevon travel, I had to use the standard throws from the instructions to avoid fouling on the vertical fins with full deflection on both channels (one up and one level). My servos are easily capable of double this amount so do I just hack away at the elevons till they clear, or will this have negative consequences that I haven't thought of?

Rather than argue the semantics, perhaps it is better to discus the effect of the motor thrust line.

The FunJet instruction say "The new design of motor
mount is very helpful , as it enables you to adjust the
downthrust easily, and the set thrust line can simply be
read off on a scale. Start by flying at full-throttle, and trim
the model accurately, i.e. straight and level “hands-off”. If
you now switch the motor off, the FunJet should make the
transition to a steady glide. If the model climbs and slows
down, the downthrust is too great - reduce the downthrust
angle. If the model goes into a dive, the downthrust is too
low - increase the downthrust slightly and add a little uptrim
before flying again. Repeat this procedure until the
model goes into a smooth descent when you close the
throttle, and responds to an open throttle by spontaneously
flying straight and level, with a slight tendency to climb."

Start off by having the marker, attached to the motor mount, at the neutral point on the scale. If the model climbs on the reduction of power as above, reduce the downthrust by rotating the adjustment scew clockwise to move the marker back towards the prop.

I had to cut away the Elevons to clear the fins.

If that is a true photograph in flight why is the pilot not fully strapped in as the only flight crew at the controls.